Confocal single-molecule fluorescence is a powerful tool for monitoring conformational dynamics, and has provided new insight into the enzymatic activities of complex biological molecules such as DNA and RNA polymerases. Though useful, such studies are typically qualitative in nature, and performed almost exclusively in highly purified, in vitro settings. In this work, I focus on improving the methodology of confocal single-molecule fluorescence in two broad ways: (i) by enabling the quantitative identification of molecular dynamics in proteins and nucleic acids in vitro, and (ii) developing the tools needed to perform these analyses in vivo. Toward the first goal, and together with several colleagues, I have developed three novel methods for the quantitative identification of dynamics in biomolecules: (i) Burst Variance Analysis (BVA), which unambiguously identifies dynamics in single-molecule FRET experiments; (ii) Dynamic Probability Density Analysis (PDA), which hypothesis-tests specific kinetic models against smFRET data and extracts rate information; and (iii) a novel molecular counting method useful for studying single-molecule thermodynamics. We validated these methods against Monte Carlo simulations and experimental DNA controls, and demonstrated their practical application in vitro by analyzing the “fingers-closing” conformational change in E.coli DNA Polymerase I; these studies identified unexpected conformational flexibility which may be important to the fidelity of DNA synthesis. To enable similar studies in the context of a living cell, we generated a nuclease-resistant DNA analogue of the Green Fluorescent Protein, or “Green Fluorescent DNA,” and developed an electroporation method to efficiently transfer it into the cytoplasm of E.coli. We demonstrate in vivo confocal detection of smFRET from this construct, which is both bright and photostable in the cellular milieu. In combination with PDA, BVA and our novel molecular counting method, this Green Fluorescent DNA should enable the characterization of DNA and protein-DNA dynamics in living cells, at the single-molecule level. I conclude by discussing the ways in which these methods may be useful in investigating the dynamics of processes such as transcription, translation and recombination, both in vitro and in vivo.

The research problem of this thesis is to explore the effects of top-down, bureaucratic definitions of belonging and social identity on urban social relations. More specifically, the thesis analyses the ways in which the nativist categorisations of indigeneity in Kano and autochtonie in Amsterdam can help to understand the tensions between ethnic groups in these two cities. Methodologically, the study is designed as a least-similar, comparative exploration and uses mixed qualitative and quantitative methods in its case studies of Kano and Amsterdam. Theoretically, this study uses identity cleavages and identification as the mediators between policy categories and social relations. It combines social-psychological, historical, and institutional theories to link bureaucratic nativism to ethnic identities and, finally, to conflictual (or ‘destructive’) interethnic relations. The resulting theoretical argument of the thesis is that nativist policy categorisations are likely conducive to antagonism, avoidance, and conflict between groups defined as ‘natives’ and ‘settlers’. The central finding of the thesis is that both in Kano and in Amsterdam, indigeneity and autochtonie have entrenched a primordial and competitive (or ‘exclusionary’) notion of ethnic identities and have thus been conducive to interethnic antagonism, avoidance, and conflict. Introduced at a time of rapid immigration, social change, and persistent horizontal inequalities, the two top-down policy categories came to redefine urban belonging in Kano and Amsterdam. As a result, previously apolitical ethnic boundaries between ‘natives’ and ‘settlers’ became politicised, connected to exclusionary definitions of religion and class, and ranked on the basis of their claim to a primordial ‘native’ status - that is, their status as historical ‘first-comers’ in their place of residence. The categorisation and group positioning effects of nativism have, therefore, intensified the urban struggle to belong in Kano and Amsterdam. At the same time, however, the thesis underlines that ethnic conflict in Kano and Amsterdam is limited, partly because nativist forms of belonging are continuously challenged by, for example, inclusive multiculturalism in Kano and urban citizenship in Amsterdam.

During human immunodeficiency virus 1 (HIV-1) infection, the viral population is in constant battle with the host immune system. The cytotoxic T-lymphocyte (CTL) response, a branch of the adaptive immune response, is implicated in viral control and can drive viral evolution in the infected host population. Endogenous viral peptides, or ‘epitopes’, are presented to CTLs by human leukocyte antigen (HLA) class I molecules on the surface of infected cells where they may be identified as non-self. Mutations in or proximal to a viral epitope can result in ‘escape’ from CTLs targeting that epitope. The repertoire of epitopes which may be presented is dependent upon host class I HLA types. As such, reversion may occur after transmission due to changes in viral fitness and selection in the context of a new HLA background. Thus, parameters describing the dynamics of CTL escape and reversion are key to understanding how CTL responses within individuals relate to HIV-1 sequence evolution in the infected host population. Escape and reversion can be studied directly using biological assays and longitudinal viral sequence data, or indirectly by considering viral sequences across multiple hosts. Indirect approaches include tree based methods which detect associations between host HLA and viral sequence but do not estimate rates of escape and reversion, and ordinary differential equation (ODE) models which estimate these rates but do not consider the dependency structure inherent in viral sequence data. We introduce two models which estimate escape and reversion rates whilst accounting for the shared ancestry of viral sequence data. For our first model, we lay out an integrated Bayesian approach which combines genealogical inference and an existing epidemiological model to inform escape and reversion rate estimates. Using this model, we find evidence for correlation between escape rate estimates across widely separated geographical regions. We also observe a non-linear negative correlation between in vitro replicative capacity and escape rate. Both findings suggest that epistasis does not play a strong role in the escape process. Although our first model worked well, it had some key limitations which we address in our second method. Notably, by making a series of approximations, we are able account for recombination and analyse very large datasets which would be computationally infeasible under the first model. We verify our second approach through extensive simulations, and use the method to estimate both drug and HLA associated selection along portions of the HIV-1 genome. We test the results of the model using existing knowledge, and determine a collection of putative selected sites which warrant further investigation. Finally, we find evidence to support the notion that the CTL response played a role in HIV-1 subtype diversification.

Tissue engineers – in order to develop therapies for the treatment of complex neurological injuries and diseases – attempt to recreate elaborate developmental mechanisms in vitro. Neuronal precursor cells are excellent candidates for the study of developmental operations such as cell adhesion, differentiation, and axonal pathfinding. Hyaluronan (HA) is a common polysaccharide that is found extensively throughout the neuronal extracellular matrix (ECM), and can be functionalised and crosslinked to form stable hydrogels that support growing neuronal cells. Hyaluronan hydrogels can be modified chemically and mechanically to mimic the ECM of the developing brain, awarding control over mechanisms such as differentiation and axonal pathfinding. This thesis is concerned with the functionalisation and characterisation of HA hydrogels, ultimately in order to simulate vital properties of the developing brain. Here we show that HA hydrogels can be finely tuned mechanically (by modulating stiffness and viscosity), and chemically, by the conjugation of peptides that mimic the neural cell adhesion molecule (NCAM). NCAM mimics and novel mimics of sialylated NCAM significantly influence the differentiation of NSPCs in 2D and 3D. HA hydrogels successfully support long term culture of neural cells in 3D, and encourage the formation and extension of neurites of several cell types including human, mouse and rat neuronal precursor and stem cells. These results demonstrate for the first time that novel NCAM mimicking peptides can be conjugated to well defined hydrogel matrices that influence intricate developmental behaviours in 3D. Understanding how neural cells form functional networks is essential for the development of clinical approaches that attempt to address the injuries and diseases that affect these systems.

Genome wide association studies (GWAS) have revolutionized our approach to mapping genetic determinants of complex human diseases. However, even with success from recent studies, we have typically been able to explain only a fraction of the trait heritability. GWAS are typically analysed by testing for the marginal effects of single variants. Consequently, it has been suggested that gene-gene interactions might contribute to the missing heritability of complex diseases. GWAS incorporating interaction effects have not been routinely applied because of statistical and computational challenges relating to the number of tests performed, genome-wide. To overcome this issue, I have developed novel methodology to allow rapid testing of pairwise interactions in GWAS of complex traits, implemented in the IntRapid software. Simulations demonstrated that the power of this approach was equivalent to computationally demanding exhaustive searches of the genome, but required only a fraction of the computing time. Application of IntRapid to GWAS of a range of complex human traits undertaken by the Wellcome Trust Case Control Consortium (WTCCC) identified several interaction effects at nominal significance, which warrant further investigation in independent studies. In an attempt to fine-map the identified interacting loci, I undertook imputation of the WTCCC genotype data up to the 1000 Genomes Project reference panel (Phase 1 integrated release, March 2012) in the neighbourhood of the lead SNPs. I modified the IntRapid software to take account of imputed genotypes, and identified stronger signals of interaction after imputation at the majority of loci, where the lead SNP often had moved by hundreds of kilobases. The X-chromosome is often overlooked in GWAS of complex human traits, primarily because of the difference in the distribution of genotypes in males and females. I have extended IntRapid to allow for interactions with the X chromosome by considering males and females separately, and combining effect estimates across the sexes in a fixed-effects meta-analysis. Application to genotype data from the WTCCC failed to identify any strong signals of association with the X-chromosome, despite known epidemiological differences between the sexes for the traits considered. The novel methods developed as part of this doctoral work enable a user friendly, computationally efficient and powerful way of implementing genome-wide gene-gene interaction studies. Further work would be required to allow for more complex interaction modelling and deal with the associated computational burden, particularly when using next-generation sequencing (NGS) data which includes a much larger set of SNPs. However, IntRapid is demonstrably efficient in exhaustively searching for pairwise interactions in GWAS of complex traits, potentially leading to novel insights into the genetic architecture and biology of human disease.

A major therapeutic challenge in musculoskeletal regenerative medicine is how to effectively replenish bone tissue lost due to pathological conditions such as fracture, osteoporosis, or rheumatoid arthritis. Mesenchymal stem cells are currently investigated for applications in bone-tissue engineering and human bone marrow-derived mesenchymal stem cells (hMSCs) could be a promising source for generation of tissue-engineered bone. However, the therapeutic potential of MSCs has not been fully exploited due to a lack of knowledge regarding the identity, nature, and differentiation of hMSCs. Epigenetic mechanisms regulating the chromatin structure as well as specific gene transcription are crucial in determination of stem cell differentiation. With the aim to systematically identify epigenetic factors that modulate MSC differentiation, the work in this thesis encompasses an approach to identify epigenetic mechanisms underlying, initiating, and promoting osteoblast differentiation, and the investigation of individual epigenetic modulators. Various osteogenic inducers were validated for differentiation of MSCs and an assay allowing assessment of differentiation outcome was developed. This assay was subsequently employed in knockdown experiments with lentiviral short hairpin RNAs and inhibitor screens with small molecules targeting putative druggable epigenetic modulator classes. This approach identified around 100 epigenetic modulator candidates involved in osteoblast differentiation, of these candidates approximately 2/3 downregulated and 1/3 upregulated alkaline phosphatase (ALP) activity. Serving as a proof-of-concept, orthogonal validation experiments employing locked nucleic acid (LNA) knockdown were performed to validate a subset of candidates. Two identified target genes were selected for further investigation. Bromodomain-containing protein 4 (BRD4) was identified as one component of epigenetic regulation; its inhibition led to a decrease in ALP expression, downregulation of key osteoblast transcription factors Runx2 and Osterix, as well as impaired bone matrix formation. Knockdown of lysine (K)-specific demethylase 1A (KDM1A/LSD1) upregulated ALP activity and treatment with a small molecule inhibitor targeting KDM1A led to an increase in ALP, RUNX2, and bone sialoprotein expression. Intriguingly, in a transgenic mouse model overexpressing Kdm1a a decrease in bone volume and bone mineral density was observed, thus supporting the hypothesis that KDM1A is a central regulator of osteoblast differentiation.

Vertebrate genomes exhibit global methylation of cytosine residues where they occur in a cytosine-guanine dinucleotide (CpG) context and this epigenetic mark is generally thought to be repressive to transcription. Punctuating this pervasive DNA methylation landscape are short, contiguous regions of non-methylated DNA which are found at two thirds of mammalian gene promoters. These non-methylated regions exhibit CpG content close to expected levels as they escape the depletion of CpGs observed across the methylated fraction of the genome. The unique nucleotide properties of these CpG island (CGI) regions enable their identification by computational prediction in mammalian genomes. Owing to a lack of high-resolution genome-wide DNA methylation profiles in non-mammalian species, these CGI predictions have often been used as a proxy for non-methylated DNA in these organisms. In contrast to mammals, CGI predictions in cold-blooded vertebrates rarely coincide with gene promoters, leading to the belief that CGls are significantly divergent between vertebrate species, and that unique promoter-associated features may have been acquired during warmblooded vertebrate evolution. This thesis is primarily concerned with the location, establishment and biological function of non-methylated islands of DNA in vertebrate genomes. To experimentally determine genome-wide profiles of non-methylated DNA, a novel biochemical technique was established called biotinylated ZF-CxxC affinity purification (Bio-CAP), and development of this method is discussed in Chapter 3. Experimental analysis of non-methylated DNA profiles in this thesis initially addresses two main questions: (1) 'How does the non-methylated DNA landscape compare genome-wide for seven vertebrates considering distinct tissue types and developmental stages?' (2) 'How are vertebrate non-methylated regions of DNA defined and interpreted in the nuclear environment?' To address the first question, non-methylated DNA was profiled by Bio-CAP sequencing across the genomes of seven diverse vertebrate species, representing all major branch points of vertebrate evolution, and the results are discussed in Chapters 4 and S. Contrary to previously held dogma, experimentally determined nonmethylated islands of DNA (NMls) constitute an ancient epigenetic feature of vertebrate gene regulatory elements. However, despite having numerous high-resolution maps of vertebrate non-methylated DNA, the means by which NMls are identified and maintained in the nuclear environment remains poorly understood. To address the second question and identify features which determine the methylation state of DNA, exogenous DNA sequences were introduced into mouse embryonic stem (ES) c~.II~. Non-methylated DNA was profiled by Bio-CAP sequencing to investigate how different features, such as sequence-specific binding motifs, chromatin architecture and nucleotide composition of a given DNA sequence impact local DNA methylation patterns. Interestingly, the majority of exogenous promoters were appropriately non-methylated in mouse ES cells, germline and somatic cells suggesting that gene promoters have retained strong signals for the nonmethylated state across millions of years of evolution (discussed in Chapter 6). During mouse embryogenesis, genome-scale DNA demethylation and remethylation events occur to remodel the epigenetic landscape and loss of DNA methylation during this time leads to embryonic lethality. To investigate the biological function of non-methylated DNA, the third question addressed in this thesis is (3) 'What is the developmental importance of non-methylated islands of DNA during vertebrate embryogenesis?' To investigate this, members of the ZF-CxxC domain-containing family of chromatin modifiers were ablated in zebrafish embryos to perturb the chromatin landscape at NMls, and therefore interfere with their function during early development (Chapter 7). Early embryonic development and patterning was disrupted in knockdown embryos, suggesting that interpretation of non-methylated DNA and placement of chromatin modifications at NMls is essential for normal zebrafish embryogenesis. Together this work sheds light on the evolutionary origins of NMls, the mechanisms involved in the recognition and establishment of nonmethylated loci and provides an insight into the function of non-methylated DNA during early embryonic development.

Membrane protein mechanotransduction is the altered function of an integral membrane protein in response to mechanical force. Such mechanosensors are found in all kingdoms of life, and increasing numbers of membrane proteins have been found to exhibit mechanosensitivity. How they mechanotransduce is an active research area and the topic of this thesis. The methodology employed is classical molecular dynamics (MD) simulations. MD systems are complex, and two programs were developed to reduce this apparent complexity in terms of both visual abstraction and statistical analysis. Bendix detects and visualises helices as cylinders that follow the helix axis, and quantifies helix distortion. The functionality of Bendix is demonstrated on the symporter Mhp1, where a state is identified that had hitherto only been proposed. InterQuant tracks, categorises and orders proximity between parts of an MD system. Results from multiple systems are statistically interrogated for reproducibility and significant differences at the resolution of protein chains, residues or atoms. Using these tools, the interaction between membrane and the Escherichia coli mechanosensitive channel of small conductance, MscS, is investigated. Results are presented for crystal structures captured in different states, one of which features electron density proposed to be lipid. MD results supports this hypothesis, and identify differential lipid interaction between closed and open states. It is concluded that propensity for lipid to leave for membrane bulk drives MscS state stability. In a subsequent study, MscS is opened by membrane surface tension for the first time in an MD setup. The gating mechanism of MscS is explored in terms of both membrane and protein deformation in response to membrane stretch. Using novel tension methodology and the longest MD simulations of MscS performed to date, a molecular basis for the Dashpot gating mechanism is proposed. Lipid emerges as an active structural element with the capacity to augment protein structure in the protein structure-function paradigm.

Globally, twenty-seven countries have resettlement programs associated with UNHCR - representing commitments to the international refugee framework and domestic commitments to those refugees resettled. Since 1975, the US has resettled over three million refugees, including over 75,000 Bhutanese refugees since 2008 - more than all other countries combined on both accounts. The US Office of Refugee Resettlement has the mandate to 'make available sufficient resources for employment training and placement in order to achieve economic self-sufficiency among refugees as quickly as possible' (The Refugee Act of 1980). Nevertheless, their economic self-sufficiency and the intertwined ideas of employment and wellbeing remain little examined. A global systematic review of available high-quality evidence examined whether interventions affect resettled refugees' economic self-sufficiency and wellbeing. Although 9,260 citations were reviewed from a wide variety of academic, policy, and grey literature, no studies met inclusion criteria. This Campbell-registered systematic review concludes that evidence is insufficient to determine if programs affect resettled refugees' economic self-sufficiency and wellbeing. Subsequently, qualitative research explored existing interventions to improve the economic self-sufficiency of resettled refugees, their theories of change, and perceptions of effectiveness in Pittsburgh, Pennsylvania. Program design follows a policy mandate and expects that initial employment leads to sustained self-sufficiency and wellbeing, albeit without measuring these outcomes or providing long-term assistance. The findings serve as a basis for future research and reveal programming implications for the Bhutanese refugee community in Pittsburgh and broadly for refugee resettlement. Next, a cross-sectional survey of 145 randomly selected Bhutanese refugees in Pittsburgh (a response rate of 92.9%) was conducted to provide groundbreaking demographics, rates of economic self-sufficiency, and correlates with improved outcomes. The population was overwhelmingly low-income with high usage of certain assistance such as food assistance. Both bivariate relationships and predictive models for employment, gross income, wages, assistance usage, and having 'enough' money to pay the bills were examined. Overall, these paint a complex picture, including the potential importance of neighborhoods, household size, and religious affiliation as well as a more typical picture of the importance of gender, education levels, and time in the country for certain measures of employment, earnings, and household self-sufficiency. The evidence-based perspective on the economic self-sufficiency of resettled refugees shows that little is known globally, including the potential for interventions to cause harm or success. Understanding the employment services and perspectives of economic self-sufficiency and wellbeing for the Bhutanese population provides a lens to view not only the challenges and successes of this population, but also national and international obligations. As one focus group participant stated, 'Government should understand the nature of the refugees arriving and put us with jobs that ... allow the life to sustain.'

This thesis addresses the role of the birth complex in Friedrich Nietzsche’s philosophy and in Richard Wagner’s operas. I see the birth complex as characterised by a dialectical relation between flesh and light, which is itself polarised by the tension between desire and anxiety. A structural determinant of the human relation to the world, this complex in my argument is of special importance for understanding the roles given to and assumed by women. Wagner gave the birth complex its first comprehensive elaboration through his operas. This, I contend, is the aspect of Wagner’s work that Nietzsche in his writings particularly reacted to through the ambivalent fascination it awakened in him. I argue that, even after Nietzsche’s break from Wagner, the birth complex remains central in his philosophy. The primary reference I build on here is Otto Rank’s theory of birth trauma, as set out in Das Trauma der Geburt (1924). To me, Rank’s theorisation of the trauma of birth is a translation into psychoanalytic language of Nietzsche’s philosophy, which itself arose with a translation into philosophical language of Wagner’s operas. In this thesis I build especially on Rank’s formulation of the tension between desire and anxiety and on his suggestions concerning the causes of the undoing of women. However, Rank did not take into account what I contend is a key aspect of both Nietzsche’s and Wagner’s work: the role of light in its dialectical relation with the flesh. By flesh I mean the interiority of the mother’s body and, by extension, the human body insofar as it is conceived through its relation to the maternal body. In the first main section of my PhD, I propose a theoretical understanding of the birth complex through an analysis of Nietzsche’s philosophy. I start with his writings pro and contra Wagner, showing that what Nietzsche primarily sees in Wagner’s operas is the birth complex. I then go on to argue that Nietzsche’s philosophy of life and of creativity is an exploration of the ways in which birth could be overcome. The second main section of my PhD is dedicated to Wagner, with largely text-based readings of three operas. I first discuss the extent to which death in Der fliegende Holländer and in the Freudian conception of the death drive is a mask for birth. I then tackle Tristan und Isolde and its famous celebration of night and death, in order to investigate whether love can be reduced to the birth complex. The last chapter of this section presents a close analysis of Das Rheingold and especially of its first scene and of Wagner’s indications on lighting. In a third and shorter section, I show that Hugo von Hofmannsthal’s and Richard Strauss’s Elektra pursued and reviewed this fundamental preoccupation of Nietzsche’s and Wagner’s work in proposing a further formulation of the birth complex that incorporates the scene of matricide. Finally, as a coda to the thesis, I explore the extent to which the uses of stage lighting pioneered by Adolphe Appia have been coming to terms with the birth complex.